[gmx-users] How to determine box shape and parameters from a run

[Mark Abraham]

So, what are the rules, so we can document them? :-) I've never needed to
work it out, but you're the man, Tsjerk ;-)

Mark

On Tue, Nov 3, 2015 at 10:23 PM Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Ramon,
>
> That's a rhombic dodecahedron with a square XY base.
>
> Cheers,
>
> Tsjerk
>
> On Tue, Nov 3, 2015 at 5:12 PM, Ramon Crehuet <rcsqtc at iqac.csic.es> wrote:
>
> > Thanks Justin,
> > The edr file is binary and I don't know how to access it.
> > I had seen that the gro file contains the vectors, and the documentation
> > says the following:
> >
> > * box vectors (free format, space separated reals), values: v1(x) v2(y)
> > v3(z) v1(y) v1(z) v2(x) v2(z) v3(x) v3(y)*
> >
> > However I still don't know what these components are and how to relate
> > that to a dodecahedron, truncated octahedron, etc.
> > In particular, my file contains:
> >
> >   13.27362  13.27362   9.38587   0.00000   0.00000   0.00000   0.00000
> > 6.63682   6.63682
> >
> > Thanks again,
> > Ramon
> >
> >
> > On 11/3/15 5:56 AM, Ramon Crehuet wrote:
> > >* Dear all,
> > *>* This is a very simple question, but I could not find the answer in
> the
> > *>* documentation. Some time ago I run a simulation and now I don't
> remember the box
> > *>* shape and sizes I used. In which file is this information contained?
> > *>* A related question is whether the box volume is printed somewhere or
> I need to
> > *>* calculate it from the parameters.
> > *>* Thanks in advance,
> > *>* Ramon
> > *>>* PS. My log contains Box-X Box-Y and Box-Z parameters. Does that
> mean I used a
> > *>* rectangular box?
> > *>
> > Box vectors are stored in the .edr file, and you can verify the shape
> from the
> > vectors printed to any coordinate file (your starting coordinates,
> dumped from
> > the .tpr if needed, or any final coordinate file printed by mdrun).
> >
> > -Justin
> >
> >
> > --
> > Ramon Crehuet
> > Cientific Titular (Assistant Professor)
> > Institute of Advanced Chemistry of Catalonia
> > IQAC - CSIChttp://www.iqac.csic.es/qteor
> https://twitter.com/rcrehuethttp://ramoncrehuet.wordpress.com/
> > Tel. +34 934006116
> > Jordi Girona 18-26
> > 08034 Barcelona (Spain)
> >
> >
> > --
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
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